We've all seen in, the very first page... THE END. Bruce is tied up, bat carved into his chest, Gotham a flame, and someone telling him that he's lost. OMINOUS!
Flash back to... the now? Jason Bard is the GCPD's newest hire from Detroit, and while he was expecting to meet the man who hired him, Bullock's the one to greet him to Gotham, as Jim Gordon is currently dealing with a Pyg infestation.
Somewhere else in Gotham, Pyg has returned to his gloriously crazy roots and is attacking Gordon and some kids with a plane that shoots syringes out of its machine gun. Yep! Crazy Pyg is back! When it looks like Gordon and the kids are doomed for, Batman makes his entrance, using the same suit he fought the Talons off with to crash Pyg's plane.
Both Batman and Gordon then give chase to Pyg's men who get split up. Batman takes Pyg, Gordon goes after the lone henchman into the subway. Once Batman ties up Pyg (yes, he makes a hog-tied pun... or says he should), he gets notice from Alfred that there's a problem in the subway, as two trains are on the same track, headed towards Gordon.
At the GCPD, Bullock brings Bard in to meet the gang, and first up is Major
Gordon has Pyg's thug he was chasing back up against a wall (with a transformer behind him), gun drawn, because that guy has a gun too. Gordon tells the thug to drop his weapon, but General Thug #4 doesn't seem to know what Gordon is talking about, claiming not to have a gun. After the count of three, Gordon fires, and shit goes real bad from there...
The bullet seemingly passes right through the guy Gordon was aiming at, hits the transformer, big explosion. Meanwhile two trains are still coming, and while Batman gets Gordon off the tracks, Alfred can't seem to take control of either and boom, head on collision, lots of people dead.
In the wreckage, Gordon is seemingly talking to himself, saying he was just trying to disarm the man... but again, seems like something is up, because Batman tells him that the man was never holding a gun. Gets even weirder, because those transformers don't seem to control anything major and shouldn't have exploded like that. Nevertheless, Major
Bard's a little taken back by his first night on the job, but Gordon tells him that he was hired for a reason and that was to do his job, and do it well. So with that, Bard reads Gordon his rights, and takes him away in cuffs.